LAMMPS (24 Mar 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units           real
atom_style      full

pair_style      lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style    pppm 0.0001

read_data       data.peptide
Reading data file ...
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     7 = max # of 1-3 neighbors
    14 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.017 seconds

neighbor        2.0 bin
neigh_modify    delay 5

timestep        2.0

thermo_style    multi
thermo          50

group tmd id 1:6
6 atoms in group tmd

fix             1 all nvt temp 275.0 275.0 100.0 tchain 1
fix             0 tmd tmd 0.1 tmd.target  100 tmd.log
Reading TMD target file tmd.target ...
fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
      19 = # of size 2 clusters
       6 = # of size 3 clusters
       3 = # of size 4 clusters
     640 = # of frozen angles
  find clusters CPU = 0.000 seconds

group           peptide type <= 12
84 atoms in group peptide

#dump           1 peptide atom 10 dump.peptide

#dump           2 peptide image 25 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify    2 pad 3

#dump           3 peptide movie 25 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify    3 pad 3

#compute                bnd all property/local btype batom1 batom2
#dump           2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]

run             300
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 4312 960
  generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond:    4   1.111     1.44264e-05        9
Bond:    6   0.996998  7.26967e-06        6
Bond:    8   1.08      1.32536e-05        6
Bond:   10   1.111     1.22749e-05        8
Bond:   12   1.08      1.11767e-05        9
Bond:   14   0.96      0                  1
Bond:   18   0.957206  4.37979e-05     1280
Angle:  31   104.519   0.00396029       640
Per MPI rank memory allocation (min/avg/max) = 16.78 | 16.97 | 17.16 Mbytes
------------ Step              0 ----- CPU =            0 (sec) -------------
TotEng   =     -5237.4580 KinEng   =      1134.9186 Temp     =       282.1005 
PotEng   =     -6372.3766 E_bond   =        16.5572 E_angle  =        36.3726 
E_dihed  =        15.5190 E_impro  =         1.9426 E_vdwl   =       692.8945 
E_coul   =     26772.2646 E_long   =    -33907.9271 Press    =      -837.0112
------------ Step             50 ----- CPU =    0.1916178 (sec) -------------
TotEng   =     -5001.6799 KinEng   =      1319.3760 Temp     =       327.9501 
PotEng   =     -6321.0559 E_bond   =        17.4415 E_angle  =        42.4509 
E_dihed  =        25.0839 E_impro  =         4.4025 E_vdwl   =       725.7619 
E_coul   =     26771.0015 E_long   =    -33907.1980 Press    =        -1.1409
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.11096   0.000146572        9
Bond:    6   0.996997  7.55911e-06        6
Bond:    8   1.08      8.22449e-06        6
Bond:   10   1.11099   3.00424e-05        8
Bond:   12   1.08      6.53505e-06        9
Bond:   14   0.95999   0                  1
Bond:   18   0.957195  4.74892e-05     1280
Angle:  31   104.52    0.00446577       640
------------ Step            100 ----- CPU =    0.3672111 (sec) -------------
TotEng   =     -5114.3221 KinEng   =      1168.2996 Temp     =       290.3979 
PotEng   =     -6282.6217 E_bond   =        45.5470 E_angle  =        87.5725 
E_dihed  =        26.1332 E_impro  =         1.8662 E_vdwl   =       791.5291 
E_coul   =     26670.6792 E_long   =    -33905.9488 Press    =       -29.3446
------------ Step            150 ----- CPU =    0.5543252 (sec) -------------
TotEng   =     -5302.3058 KinEng   =      1211.4300 Temp     =       301.1186 
PotEng   =     -6513.7358 E_bond   =        51.4069 E_angle  =        82.5752 
E_dihed  =        31.1298 E_impro  =         4.3390 E_vdwl   =       764.0550 
E_coul   =     26461.8975 E_long   =    -33909.1392 Press    =     -1204.2714
SHAKE stats (type/ave/delta/count) on step 200
Bond:    4   1.11094   0.000292869        9
Bond:    6   0.996989  3.13206e-05        6
Bond:    8   1.07999   4.4723e-05         6
Bond:   10   1.111     1.08895e-05        8
Bond:   12   1.07999   1.42694e-05        9
Bond:   14   0.959976  0                  1
Bond:   18   0.957195  8.58257e-05     1280
Angle:  31   104.52    0.00597861       640
------------ Step            200 ----- CPU =    0.7449468 (sec) -------------
TotEng   =     -5785.4658 KinEng   =      1048.7220 Temp     =       260.6751 
PotEng   =     -6834.1878 E_bond   =        21.7304 E_angle  =        48.3249 
E_dihed  =        20.5973 E_impro  =         2.0603 E_vdwl   =       818.9173 
E_coul   =     26165.9673 E_long   =    -33911.7854 Press    =     -1228.5754
------------ Step            250 ----- CPU =    0.9417257 (sec) -------------
TotEng   =     -6108.4577 KinEng   =       828.5246 Temp     =       205.9418 
PotEng   =     -6936.9823 E_bond   =        26.5971 E_angle  =        68.2771 
E_dihed  =        36.1232 E_impro  =         5.2092 E_vdwl   =       884.1146 
E_coul   =     25955.7302 E_long   =    -33913.0338 Press    =     -1365.4736
SHAKE stats (type/ave/delta/count) on step 300
Bond:    4   1.11174   0.0109854          9
Bond:    6   0.996999  1.94775e-06        6
Bond:    8   1.08      3.97089e-06        6
Bond:   10   1.111     2.52634e-06        8
Bond:   12   1.08      1.24445e-06        9
Bond:   14   0.96      0                  1
Bond:   18   0.9572    1.22873e-05     1280
Angle:  31   104.52    0.0013486        640
------------ Step            300 ----- CPU =     1.137003 (sec) -------------
TotEng   =     -5492.5016 KinEng   =      1315.6899 Temp     =       327.0339 
PotEng   =     -6808.1915 E_bond   =        88.7968 E_angle  =       104.4228 
E_dihed  =        28.2384 E_impro  =        43.5061 E_vdwl   =       992.5315 
E_coul   =     25849.1499 E_long   =    -33914.8370 Press    =       268.8010
Loop time of 1.13706 on 4 procs for 300 steps with 2004 atoms

Performance: 45.591 ns/day, 0.526 hours/ns, 263.838 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.75407    | 0.80373    | 0.84144    |   3.6 | 70.68
Bond    | 0.0010088  | 0.0024668  | 0.0045274  |   2.6 |  0.22
Kspace  | 0.095468   | 0.13434    | 0.18276    |   8.9 | 11.81
Neigh   | 0.13509    | 0.13515    | 0.13522    |   0.0 | 11.89
Comm    | 0.024217   | 0.025086   | 0.026404   |   0.5 |  2.21
Output  | 0.00020952 | 0.00023591 | 0.00031389 |   0.0 |  0.02
Modify  | 0.033319   | 0.033374   | 0.033436   |   0.0 |  2.94
Other   |            | 0.00268    |            |       |  0.24

Nlocal:            501 ave         530 max         459 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost:        6562.75 ave        6755 max        6370 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs:         177696 ave      195050 max      158403 min
Histogram: 1 0 0 1 0 0 0 1 0 1

Total # of neighbors = 710782
Ave neighs/atom = 354.68164
Ave special neighs/atom = 2.3403194
Neighbor list builds = 32
Dangerous builds = 1

Total wall time: 0:00:01
